3B1D | pdb_00003b1d

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External aldimine form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	22% PEG 8000, 0.1M Hepes pH7.5, 0.08M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.965	α = 90
b = 111.302	β = 90
c = 217.193	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2008-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.66	36.84	99.2	0.072	0.072	7.9	14.7	189945	189945

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.7	98.3		0.248	0.248	3.1	14.6	13790

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.66	36.84	179903	179903	9529	100	0.15229	0.15229	0.15097	0.1596	0.1773	0.1832	RANDOM	9.178

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.73			-0.21		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.545
r_dihedral_angle_4_deg	15.596
r_dihedral_angle_3_deg	11.627
r_dihedral_angle_1_deg	5.842
r_scangle_it	3.282
r_scbond_it	2.041
r_angle_refined_deg	1.318
r_mcangle_it	1.178
r_angle_other_deg	0.921
r_mcbond_it	0.62
r_chiral_restr	0.242
r_symmetry_vdw_other	0.223
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.197
r_nbd_other	0.187
r_nbtor_refined	0.18
r_mcbond_other	0.169
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.131
r_nbtor_other	0.083
r_metal_ion_refined	0.057
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12484
Nucleic Acid Atoms
Solvent Atoms	1616
Heterogen Atoms	287

Software

Software
Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling